Search

While genetic analyses have revealed ~100 risk loci associated with osteoarthritis (OA), only eight have been linked to hand OA. Besides, these studies were performed in predominantly European and Caucasian ancestries. Here, we conducted a genome-wide association study in the Han Chinese population to identify genetic variations associated with the disease. We recruited a total of 1136 individuals (n = 420 hand OA-affected; n = 716 unaffected control subjects) of Han Chinese ancestry. We carried out genotyping using Axiom Asia Precisi on Medicine Research Array, and we employed the RegulomeDB database and RoadMap DNase I Hypersensitivity Sites annotations to further narrow down our potential candidate variants. Genetic variants identified were tested in the Geisinger’s hand OA cohort selected from the Geisinger MyCode community health initiative (MyCode®). We also performed a luciferase reporter assay to confirm the potential impact of top candidate single-nucleotide polymorphisms (SNPs) on hand OA. We identified six associated SNPs (p-value = 6.76 × 10−7–7.31 × 10−6) clustered at 2p13.2 downstream of the CYP26B1 gene. The strongest association signal identified was rs883313 (p-value = 6.76 × 10−7, odds ratio (OR) = 1.76), followed by rs12713768 (p-value = 1.36 × 10−6, OR = 1.74), near or within the enhancer region closest to the CYP26B1 gene. Our findings showed that the major risk-conferring CC haplotype of SNPs rs12713768 and rs10208040 [strong linkage disequilibrium (LD); D’ = 1, r2 = 0.651] drives 18.9% of enhancer expression activity. Our findings highlight that the SNP rs12713768 is associated with susceptibility to and severity of hand OA in the Han Chinese population and that the suggested retinoic acid signaling pathway may play an important role in its pathogenesis.

Nutrient pollution released from highly accumulated swine wastewater is getting concerned due to global warming and waterbody harmful. Traditional combination of nitrification and denitrification is commonly applied to remove carbon and nitrogen compounds resided in various wastewater with disadvantages of high cost and energy requirements. This study applied the thermophilic flat panel photobioreactor (tFPBR) with high growth rate of TCL-1 culture to evaluate the efficiency of inorganic carbon and nitrogen transformation. This 12-h operation resulted that TCL-1 enriched batch, grown in 50 °C and alkaline environment with 1,000 µE/m2/s light intensity, had high potential for CO2 fixation rate of 122.29 ± 9.93 mg/L/h and nitrogen removal rate of 7.76 mg-N/L/h treating swine wastewater, in comparison with comprehensive community involved in carbon and nitrogen cycles in the field-scale anoxic tank. This study provided the Rapid-growing photosynthetic cyanobacteria in place of slow-growing autotrophic microbes for of carbon and nitrogen transformation in the wastewater system.

This article reviews the current developments in genus Dehalococcoides as key dechlorinating bacteria in chlorinated ethene contaminated sites. The presence of chlorinated ethenes in environment had been a concern for more than five decades as it represents significant threat to human and ecological health due to its extreme toxicity. This review elucidates the kinetics of Dehalococcoides spp. growth and compound utilization in dechlorination of chlorinated ethenes compounds. The metabolic pathways in physiology of Dehalococcoides spp. are important in the transformation of chlorinated species. The potential of isolates and its reductive dehalogenase genes are seen to infer activities of Dehalococcoides spp. that would be used to the development of engineered systems. This system is helpful in making decision on bioremediation option to treat the contaminated groundwater. Hence, the role of Dehalococcoides spp. in chlorinated ethene biodegradation is controlled by kinetics in complex ways. Therefore, intensive in-situ characterization and understanding the microbial growth on dechlorination evaluation are essential to develop a consistent and rational engineered system. This is to achieve a successful bioremediation strategies for sites contaminated with chlorinated ethenes.

Aim: This study aimed to determine clinical utility of genotype-guided dosing for warfarin in Han-Chinese. Methods: A total of 320 patients were randomly assigned International Warfarin Pharmacogenetic Consortium algorithm, Taiwan algorithm and optimal clinical care arms. The primary outcome of the study was the percentage of time in the therapeutic range during the first 90 days of treatment. Results: The percentage of time in the therapeutic range of the clinical care group in the first 2 weeks was significantly higher than the algorithm groups. This difference was no longer observed after 4 weeks. No difference in excessive anticoagulation (international normalized ratio ≥4.0) and adverse events was observed. Conclusion: Genotype-guided dosing did not provide significant benefit. Loading dose with frequent international normalized ratio monitoring could provide sufficient control of anticoagulation.

The anaerobic ammonium oxidation (anammox) process is widely acknowledged to be susceptible to a wide range of environmental factors given the slow growth rate of the anammox bacteria. Surprisingly there is limited experimental data regarding the susceptibility of the anammox process to feed starvations which may be encountered in full-scale applications. Therefore, a study was established to investigate the impact of feed starvations on nitritation and anammox activity in a demonstration-scale sequencing batch reactor. Three starvation periods were trialled, lasting one fortnight (15 d), one month (33 d) and two months (62 d). Regardless of the duration of the starvation period, assessment of the ammonia removal performance demonstrated nitritation and anammox activity were reinstated within one day of recovery operation. Characterisation of the community structure using 16S rRNA and functional genes specific for nitrogen-related microbes showed there was no clear impact or shift in the microbial populations between starvation and recovery phases. Refereed/Peer-reviewed

Background Carbamazepine, an anticonvulsant and a mood-stabilizing drug, is the main cause of the Stevens–Johnson syndrome (SJS) and its related disease, toxic epidermal necrolysis (TEN), in Southeast Asian countries. Carbamazepine-induced SJS–TEN is strongly associated with the HLA-B*1502 allele. We sought to prevent carbamazepine-induced SJS–TEN by using HLA-B*1502 screening to prospectively identify subjects at genetic risk for the condition. Methods From 23 hospitals in Taiwan, we recruited 4877 candidate subjects who had not taken carbamazepine. We genotyped DNA purified from the subjects' peripheral blood to determine whether they carried the HLA-B*1502 allele. Those testing positive for HLA-B*1502 (7.7% of the total) were advised not to take carbamazepine and were given an alternative medication or advised to continue taking their prestudy medication; those testing negative (92.3%) were advised to take carbamazepine. We interviewed the subjects by telephone once a week for 2 months to monitor them ...

Objectives To characterize a large extended family with early-onset OA of the knee and investigate its associations with the COL2A1 gene. Methods Phenotype assessments were conducted in a six-generation family to identify individuals affected with OA. Short tandem repeat polymorphic (STRP) markers and DNA sequencing were performed to investigate the involvement of the COL2A1 gene in this family. Results The kindred affected with OA showed autosomal dominant inheritance. The mean age of onset was 37.3 +/- 19.2, 29.8 +/- 13.7 and 12.0 +/- 7.2 years for generations IV, V and VI, respectively, and 25 +/- 16.1 years for males and 34.3 +/- 15.5 years for females. The height of the affected males was shorter than the unaffected males (155.9 +/- 11.4 vs 164.5 +/- 16.0 cm, P = 0.010). Arm span in the affected males was also significantly shorter than the unaffected males (158.4 +/- 12.5 vs 165.3 +/- 16.7 cm, P = 0.027). However, both height and arm span were not reduced in the affected female OA patients. STRP markers surrounding COL2A1 locus did not show linkage of the COL2A1 locus with the OA. Sequencing of COL2A1 gene revealed three single nucleotide polymorphisms but no mutation was found in the affected patients. Conclusions The COL2A1 was not a susceptibility gene responsible for the OA phenotype in a large extended kindred with familial early-onset OA. The availability of DNA samples will allow genome-wide linkage study to identify the susceptibility locus.

Objective To evaluate the use of prospective screening for the HLA-B*58:01 allele to identify Taiwanese individuals at risk of severe cutaneous adverse reactions (SCARs) induced by allopurinol treatment. Design National prospective cohort study. Setting 15 medical centres in different regions of Taiwan, from July 2009 to August 2014. Participants 2926 people who had an indication for allopurinol treatment but had not taken allopurinol previously. Participants were excluded if they had undergone a bone marrow transplant, were not of Han Chinese descent, and had a history of allopurinol induced hypersensitivity. DNA purified from 2910 participants’ peripheral blood was used to assess the presence of HLA-B*58:01. Main outcome measures Incidence of allopurinol induced SCARs with and without screening. Results Participants who tested positive for HLA-B*58:01 (19.6%, n=571) were advised to avoid allopurinol, and were referred to an alternate drug treatment or advised to continue with their prestudy treatment. Participants who tested negative (80.4%, n=2339) were given allopurinol. Participants were interviewed once a week for two months to monitor symptoms. The historical incidence of allopurinol induced SCARs, estimated by the National Health Insurance research database of Taiwan, was used for comparison. Mild, transient rash without blisters developed in 97 (3%) participants during follow-up. None of the participants was admitted to hospital owing to adverse drug reactions. SCARs did not develop in any of the participants receiving allopurinol who screened negative for HLA-B*58:01. By contrast, seven cases of SCARs were expected, based on the estimated historical incidence of allopurinol induced SCARs nationwide (0.30% per year, 95% confidence interval 0.28% to 0.31%; P=0.0026; two side one sample binomial test). Conclusions Prospective screening of the HLA-B*58:01 allele, coupled with an alternative drug treatment for carriers, significantly decreased the incidence of allopurinol induced SCARs in Taiwanese medical centres.

Aim: Acute urticaria/angioedema (AUA) induced by cross-intolerance to NSAIDs is the most frequent clinical entity in hypersensitivity reactions to drugs. In this work, we conducted a genome-wide association study in Spanish and Han Chinese patients suffering from NSAID-induced AUA. Materials & methods: A whole-genome scan was performed on a total of 232 cases (112 Spanish and 120 Han Chinese) with NSAID-induced AUA and 225 unrelated controls (124 Spanish and 101 Han Chinese). Results: Although no polymorphism reached genome-wide significance, we obtained suggestive associations for three clusters in the Spanish group (RIMS1, BICC1 and RAD51L 1) and one region in the Han Chinese population (ABI3BP). Five regions showed suggestive associations after meta-analysis: HLF, RAD51L1, COL24A1, GalNAc-T13 and FBXL7. A majority of these genes are related to Ca2+, cAMP and/or P53 signaling pathways. Conclusion: The associations described were different from those related to the metabolism of arachidonic acid and could provide new mechanisms underlying NSAID-induced AUA. Original submitted 7 June 2013; Revision submitted 19 August 2013

Degradation of terephthalate (TA) through microbial syntrophy under moderately thermophilic (46 to 50°C) methanogenic conditions was characterized by using a metagenomic approach (A. Lykidis et al., ISME J. 5:122–130, 2011). To further study the activities of key microorganisms responsible for the TA degradation, community analysis and shotgun proteomics were used. The results of hierarchical oligonucleotide primer extension analysis of PCR-amplified 16S rRNA genes indicated that Pelotomaculum , Methanosaeta , and Methanolinea were predominant in the TA-degrading biofilms. Metaproteomic analysis identified a total of 482 proteins and revealed a distinctive distribution pattern of microbial functions expressed in situ . The results confirmed that TA was degraded by Pelotomaculum spp. via the proposed decarboxylation and benzoyl-coenzyme A-dependent pathway. The intermediate by-products, including acetate, H 2 /CO 2 , and butyrate, were produced to support the growth of methanogens, as well as other microbial populations that could further degrade butyrate. Proteins related to energy production and conservation, and signal transduction mechanisms (that is, chemotaxis, PAS/GGDEF regulators, and stress proteins) were highly expressed, and these mechanisms were important for growth in energy-limited syntrophic ecosystems.

Purpose To identify the genetic cause in five families with autosomal recessive retinitis pigmentosa, a genetic disorder involving retinal degeneration and visual loss with high genetic heterogeneity. Methods We performed whole-genome single nucleotide polymorphism genotyping on 35 members from the five families to map the region of homozygosity shared by all patients. Whole-genome sequencing was then conducted on one of the patients and a novel variant was identified in POMGNT1 from the homozygous region, which was confirmed by Sanger sequencing and sequenced in all family members. Mutant and wild-type POMGNT1 were expressed in heterologous cells to assess enzyme activity. Results A 1.8-Mb homozygous region was identified at 1p34-p33 shared by all 17 patients. Whole-genome sequencing revealed a novel missense mutation in POMGNT1 (c.359A>C, p.Leu120Arg) from this homozygous region, which was shown to co-segregate with disease phenotype. The mutant protein carrying this missense mutation showed an approximately 80% decrease in POMGNT1 enzyme activity compared with the wild type. Conclusions We identified a novel mutation in POMGNT1 that causes nonsyndromic autosomal recessive retinitis pigmentosa, adding to the genetic heterogeneity of this retinal disease. POMGNT1 encodes a glycosyltransferase in O-mannosyl glycosylation and was previously found to be responsible for a group of congenital muscular dystrophies called dystroglycanopathies. Our discovery suggests the involvement of O-mannosyl glycosylation in retinitis pigmentosa and presents an instance of POMGNT1 mutation that does not involve muscular dystrophy.

Warfarin, a widely prescribed oral anticoagulant, is used for the prevention of thromboembolism. Polymorphisms in CYP2C9 and VKORC1 have been shown to be associated with warfarin dose requirements. However, it is likely that other genes could also affect warfarin dose. Aims: In this study, we aimed to identify additional genes influencing warfarin dosing in the Han-Chinese population. Materials & methods: In this study, we screened for SNPs in 13 genes (VKORC1, CYP2C9, CYP2C18, PROC, APOE, EPHX1, CALU, GGCX, ORM1, ORM2, factor II, factor VII and CYP4F2) and tested their associations with warfarin dosing with univariate and multiple regression analysis. Results: Polymorphisms in the VKORC1 gene have the strongest effects on warfarin dose, followed by CYP2C9*3. In addition, our results showed that CYP2C18, PROC and EPHX1 have small but significant associations with warfarin dose. In multiple regression analysis, PROC and EPHX1 explained 3% of the dose variation. The incorporation of these two genes into warfarin dosing algorithms could improve the accuracy of prediction in the Han-Chinese population.

Aims: Warfarin, a widely prescribed oral anticoagulant, is used for the prevention of thromboembolism. Several polymorphisms in VKORC1 have been shown to be associated with warfarin dose requirements. The frequencies of these VKORC1 polymorphisms display population differences; however, this has not been examined in many populations. In this study, we examined VKORC1 polymorphisms in five East-Asian populations (Han Chinese, Indonesian, Filipino, Thai and Vietnamese) and Indians. Materials & methods: A total of six SNPs in the VKORC1 gene (-1639G>A, 497T>G, 1173C>T, 1542T>G, 2255C>T and 3730G>A) were genotyped. Frequencies, linkage disequilibrium and haplotype structures of these six VKORC1 SNPs were analyzed. Results: Our data showed that 497T>G is only polymorphic in the Indian population. The 497G allele is very rare in the East-Asian populations (frequency < 1%). The remaining SNPs demonstrated high linkage disequilibrium and had similar frequencies and haplotype structures in all but the Indian population. The Indian population is mostly made up of the H7 haplotype (76%) while the rest of the recruited populations consisted of the H1 haplotype (>80%).

p olymorphisms in C yp 2C9 and VK or C1 have been shown to be associated with warfarin dose requirements and could be used to predict warfarin dose. We conducted a prospective study in which warfarin dose was prescribed based on C yp2C9 and VK or C1 polymorphisms in 108 han-Chinese patients without prior warfarin treatments. u sing the genotype-based dosing, 83% of patients reached stable, therapeutic international normalized ratio ( inr ) within 2 weeks of treatment initiation and none of the patients developed clinical bleeding or thromboembolic event. Ten percent (11) of patients with inr >4 and no clinical bleeding were detected during this study. at 12 weeks, 69% of the patients’ maintenance doses matched the prediction. Dosing algorithms incorporating genetic factors, age, and body surface area were developed, which could explain up to 62% of the total variation (R 2 of 0.62). This study demonstrated that pharmacogenetics-based dosing could improve time to stable, therapeutic inr , reduce adverse events, and achieve high sensitivity.

We previously reported that partial nitrification in the down-flow hanging sponge (DHS) system was satisfactorily accomplished under oxygen-limited conditions [Chuang et al., Water Res., 41, 295–302 (2007)]. In this study, we investigated the microbes that are responsible for the partial nitrification in this unique system by 16S rRNA- and amoA-based cloning analyses and fluorescence in situ hybridization. Microbes related to Nitrosomonas species were found to be chiefly responsible for catalyzing the partial nitrification. Microbes affiliated with the uncultivated phyla OP10 and Bacteroidetes were also numerous in the DHS, but their ecological niches are still unknown.

Combining the processes of partial nitrification and anaerobic ammonium oxidation (ANAMMOX) is an attractive wastewater-treatment technology for nitrogen removal. In this study we investigated partial nitrification by implementing a closed down-flow hanging sponge (DHS) reactor operated at controlled oxygen concentrations. Basic concept of DHS process is similar to that of trickling filter, in which oxygen concentration can be easily manipulated by controlling airflow to the reactor. The closed reactor was fed with artificial wastewater containing NH(4)Cl and operated with an HRT of 1.5h at 30 degrees C. Oxygen inside the reactor was maintained below 3% (1.2mgDO x L(-1)) (DO-dissolved oxygen) except during the startup periods. Five months of continuous operation showed that there was a strong relationship between oxygen concentration and nitrite production. The ratio of nitrite produced relative to ammonium oxidized increased by decreasing oxygen concentration. Partial nitrification was satisfactorily accomplished under oxygen limitation at around 0.5% in the gas phase (0.2mgDOL(-1)). The system showed a high ammonium-removal rate, at a maximum of 1.46kg NH(4)(+)-Nm(-3)day(-1), even at limited oxygen concentration. We also found that oxygen concentration played an important role in the production of nitrous oxide, which increased with decreasing oxygen concentration.

Summary Objective To evaluate the interaction of articular cartilage (AC) and subchondral bone (SB) through analysis of osteoarthritis (OA)-related genes of site-matched tissue. Design We developed a novel method for isolating site-matched overlying AC and underlying SB from three and four regions of interest respectively from the human knee tibial plateau ( n = 50). For each site, the severity of cartilage changes of OA were assessed histologically, and the severity of bone abnormalities were assessed by microcomputed tomography. An RNA isolation procedure was optimized that yielded high quality RNA from site-matched AC and SB tibial regions. Quantitative polymerase chain reaction (Q-PCR) analysis was performed to evaluate gene expression of 61 OA-associated genes for correlation with cartilage integrity and bone structure parameters. Results A total of 27 (44%) genes were coordinately up- or down-regulated in both tissues. The expression levels of 19 genes were statistically significantly correlated with the severity of AC degeneration and changes of SB structure; these included: ADAMTS1 , ASPN , BMP6 , BMPER , CCL2 , CCL8 , COL5A1 , COL6A3 , COL7A1 , COL16A1 , FRZB , GDF10 , MMP3 , OGN , OMD , POSTN , PTGES , TNFSF11 and WNT1 . Conclusions These results provide a strategy for identifying targets whose modification may have the potential to ameliorate pathological alterations and progression of disease in both AC and SB simultaneously. In addition, this is the first study, to our knowledge, to overcome the major difficulties related to isolation of high quality RNA from site-matched joint tissues. We expect this method to facilitate advances in our understanding of the coordinated molecular responses of the whole joint organ.

Introduction The aim of this study was to evaluate, for the first time, the differences in gene expression profiles of normal and osteoarthritic (OA) subchondral bone in human subjects. Methods Following histological assessment of the integrity of overlying cartilage and the severity of bone abnormality by micro-computed tomography, we isolated total RNA from regions of interest from human OA (n = 20) and non-OA (n = 5) knee lateral tibial (LT) and medial tibial (MT) plateaus. A whole-genome profiling study was performed on an Agilent microarray platform and analyzed using Agilent GeneSpring GX11.5. Confirmatory quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis was performed on samples from 9 OA individuals to confirm differential expression of 85 genes identified by microarray. Ingenuity Pathway Analysis (IPA) was used to investigate canonical pathways and immunohistochemical staining was performed to validate protein expression levels in samples. Results A total of 972 differentially expressed genes were identified (fold change ≥ ± 2, P ≤0.05) between LT (minimal degeneration) and MT (significant degeneration) regions from OA samples; these data implicated 279 canonical pathways in IPA. The qRT-PCR data strongly confirmed the accuracy of microarray results (R2 = 0.58, P